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comparison qiime_feature-table_group.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-table_group" name="qiime feature-table group" version="2018.4">
3 <description> - Group samples or features by a metadata column</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime feature-table group --i-table=$itable
10
11 #def list_dict_to_string(list_dict):
12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
13 #for d in list_dict[1:]:
14 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
15 #end for
16 #return $file_list
17
18 #end def
19 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --p-mode=$pmode --m-metadata-column="$mmetadatacolumn" --p-axis=$paxis
20 #if str($cmdconfig) != 'None':
21 --cmd-config=$cmdconfig
22 #end if
23 --o-grouped-table=ogroupedtable;
24 cp ogroupedtable.qza $ogroupedtable;
25 ]]>
26 </command>
27 <inputs>
28 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The table to group samples or features on. [required]" name="itable" optional="False" type="data"/>
29
30 <param label="--p-axis: Along which axis to group. Each ID in the
31 given axis must exist in `metadata`.
32 [required]" name="paxis" optional="False" type="select">
33 <option value="sample">sample</option>
34 <option value="feature">feature</option>
35 </param>
36
37 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
38 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
39 </repeat>
40
41 <param label="--m-metadata-column: MetadataColumn[Categorical] Column from metadata file or artifact viewable as metadata. A column defining the groups. Each unique value will become a new ID for the table on the given `axis`. [required]" name="mmetadatacolumn" optional="False" type="text"/>
42
43 <param label="--p-mode: How to combine samples or features within a
44 group. `sum` will sum the frequencies across
45 all samples or features within a group;
46 `mean-ceiling` will take the ceiling of the
47 mean of these frequencies; `median-ceiling`
48 will take the ceiling of the median of these
49 frequencies. [required]" name="pmode" optional="False" type="select">
50 <option value="median-ceiling">median-ceiling</option>
51 <option value="mean-ceiling">mean-ceiling</option>
52 <option value="sum">sum</option>
53 </param>
54
55 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
56 </inputs>
57 <outputs>
58 <data format="qza" label="${tool.name} on ${on_string}: grouped-table.qza" name="ogroupedtable"/>
59 </outputs>
60 <help>
61 <![CDATA[
62 Group samples or features by a metadata column
63 -----------------------------------------------
64
65 Group samples or features in a feature table using metadata to define the
66 mapping of IDs to a group.
67
68 Parameters
69 ----------
70 table : FeatureTable[Frequency]
71 The table to group samples or features on.
72 axis : Str % Choices({'feature', 'sample'})
73 Along which axis to group. Each ID in the given axis must exist in
74 `metadata`.
75 metadata : MetadataColumn[Categorical]
76 A column defining the groups. Each unique value will become a new ID
77 for the table on the given `axis`.
78 mode : Str % Choices({'mean-ceiling', 'median-ceiling', 'sum'})
79 How to combine samples or features within a group. `sum` will sum the
80 frequencies across all samples or features within a group; `mean-
81 ceiling` will take the ceiling of the mean of these frequencies;
82 `median-ceiling` will take the ceiling of the median of these
83 frequencies.
84
85 Returns
86 -------
87 grouped_table : FeatureTable[Frequency]
88 A table that has been grouped along the given `axis`. IDs on that axis
89 are replaced by values in the `metadata` column.
90 ]]>
91 </help>
92 </tool>